The recent explosion in genomic sequencing has deposited a wealth of information in the hands of researchers. However, there is not yet a means to efficiently analyze such data to identify which antigens among many thousands are appropriate targets for vaccine development.
More than 5000 proteins are expressed during the life cycle of the Plasmodium spp. parasite. Subunit vaccines currently in development are based on a single or few antigens and may therefore, elicit too narrow a breadth of response, providing neither optimal protection nor protection on genetically diverse backgrounds. By contrast, to duplicate the protection induced by whole organism vaccination (Good, M. F. & Doolan, D. L. Immune effector mechanisms in malaria. Curr. Opin. Immunol. 11, 412-419 (1999)), a malaria vaccine targeting an unprecedented number of parasite-derived proteins through inclusion of their minimal CD8+ and CD4+ T cell epitopes in a multiepitope construct appears to be required. However, the antigens mediating whole organism induced protection are largely unknown.
Because of various factors, principally related to antigen abundance and immunodominance, not all possible antigens are recognized by natural immunity (Yewdell J W, Bennink J R. Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. Annu. Rev. Immunol. 17, 51-88. (1999)). Various approaches have been proposed for antigen identification, including expression cloning (Kawakami, Y. & Rosenberg, S. A. Immunobiology of human melanoma antigens MART-1 and gp100 and their use for immuno-gene therapy. Int. Rev. Immunol. 14, 173-192 (1997)), elution and mass spectrometry sequencing of naturally processed MHC-bound peptides (Rotzschke, O. et al. Isolation and analysis of naturally processed viral peptides as recognized by cytotoxic T cells. Nature 348, 252-254 (1990); van Bleek, G. M. & Nathenson, S. G. Isolation of an endogenously processed immunodominant viral peptide from the class I H-2 Kb molecule. Nature 348, 213-216 (1990); Hunt, D. F. et al. Peptides presented to the immune system by the murine class II major histocompatibility complex molecule I-Ad. Science 256, 1817-1820 (1992); Cox, A. L. et al. Identification of a peptide recognized by five melanoma-specific human cytotoxic T cell lines. Science 264, 716-719 (1994)), in vitro testing of pools of overlapping peptides (Kern, F. et al. Cytomegalovirus (CMV) Phosphoprotein 65 Makes a Large Contribution to Shaping the T Cell Repertoire in CMV-Exposed Individuals. J. Infect. Dis. 185, 1709-1716 (2002)), and reverse immunogenetics (Davenport, M. P. & Hill, A. V. Reverse immunogenetics: from HLA-disease associations to vaccine candidates. Mol. Med. Today 2, 38-45 (1996); Aidoo, M. et al. Identification of conserved antigenic components for a cytotoxic T lymphocyte-inducing vaccine against malaria. Lancet 345, 1003-1007 (1995)). However, these methods suffer from potential problems such as the repeated identification of the same (frequent/dominant) epitope, biases at the level of expansion of T cell populations, and use of clonal/oligoclonal T cells. They also tend to underestimate the complexity of responses, and are not able to analyze a large number of potential targets in the context of multiple HLA types. Finally, none of these approaches easily lends itself towards the daunting task of efficiently analyzing large amounts of genomic sequence data.